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comparison cnv.xml @ 3:1ddff01fee0b draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/delly commit 57b50253f326baf18bfbf417d8c788b4f5ba66e6
author iuc
date Mon, 27 Jun 2022 18:14:59 +0000
parents 705c366c2bcc
children
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2:259b3fabd7b0 3:1ddff01fee0b
6 <import>macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <expand macro="version_command"/> 9 <expand macro="version_command"/>
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 @SINGLE_BAM@
12 @FASTA@
13 ln -s '$generic.mappability' mappability.fa &&
14
11 ## run 15 ## run
12 delly cnv 16 delly cnv
13 ## generic options 17 ## generic options
14 --genome '$generic.genome' 18 --genome genome.fa
15 --quality '$generic.quality' 19 --quality '$generic.quality'
16 --mappability '$generic.mappability' 20 --mappability mappability.fa
17 --ploidy $generic.ploidy 21 --ploidy $generic.ploidy
18 --outfile 'result.bcf' 22 --outfile 'result.bcf'
19 --covfile 'result.gz' 23 --covfile 'result.gz'
20 ## cnv calling options 24 ## cnv calling options
21 --sdrd $cnv.sdrd 25 --sdrd $cnv.sdrd
44 #end if 48 #end if
45 --mad-cutoff $gc.madcutoff 49 --mad-cutoff $gc.madcutoff
46 --percentile $gc.percentile 50 --percentile $gc.percentile
47 $gc.nowindowselection 51 $gc.nowindowselection
48 ## input 52 ## input
49 '$input' 53 'input.bam'
50 54
51 ## postprocessing 55 ## postprocessing
52 @LOG@ 56 @LOG@
53 ]]></command> 57 ]]></command>
54 <inputs> 58 <inputs>
160 <section name="oo"> 164 <section name="oo">
161 <param name="out" value="cnv,coverage,log"/> 165 <param name="out" value="cnv,coverage,log"/>
162 </section> 166 </section>
163 <output name="out_cnv"> 167 <output name="out_cnv">
164 <assert_contents> 168 <assert_contents>
165 <has_size value="700" delta="10"/> 169 <has_size value="645" delta="10"/>
166 </assert_contents> 170 </assert_contents>
167 </output> 171 </output>
168 <output name="out_coverage"> 172 <output name="out_coverage">
169 <assert_contents> 173 <assert_contents>
170 <has_size value="61"/> 174 <has_size value="61"/>